Created
July 2, 2012 23:02
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Java example of how to write a very basic OMERO importer (see https://www.openmicroscopy.org/community/viewtopic.php?f=6&t=1062)
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import ome.formats.OMEROMetadataStoreClient; | |
import ome.formats.importer.IObservable; | |
import ome.formats.importer.IObserver; | |
import ome.formats.importer.ImportCandidates; | |
import ome.formats.importer.ImportConfig; | |
import ome.formats.importer.ImportContainer; | |
import ome.formats.importer.ImportEvent; | |
import static ome.formats.importer.ImportEvent.IMPORT_DONE; | |
import ome.formats.importer.ImportLibrary; | |
import ome.formats.importer.OMEROWrapper; | |
import ome.formats.importer.cli.ErrorHandler; | |
public class simple_importer { | |
public static ImportConfig config(String[] args) throws Exception { | |
try { | |
final String host = args[0]; | |
final Integer port = Integer.valueOf(args[1]); | |
final String username = args[2]; | |
final String password = args[3]; | |
final Long datasetId = Long.valueOf(args[4]); | |
final String atLeastOneFile = args[5]; | |
final ImportConfig config = new ImportConfig(); | |
config.email.set(""); | |
config.sendFiles.set(true); | |
config.sendReport.set(false); | |
config.contOnError.set(false); | |
config.debug.set(false); | |
config.hostname.set(host); | |
config.port.set(port); | |
config.username.set(username); | |
config.password.set(password); | |
config.targetClass.set("omero.model.Dataset"); | |
config.targetId.set(datasetId); | |
return config; | |
} catch (Exception e) { | |
System.err.println("Usage: simple_importer host port user pass id file1 [file2 ...]"); | |
System.err.println("---------------------------------------------------------------"); | |
throw e; | |
} | |
} | |
public static void main(String[] args) throws Exception { | |
ImportConfig config = config(args); | |
OMEROMetadataStoreClient store = config.createStore(); | |
final String[] paths = new String[args.length-5]; | |
System.arraycopy(args, 5, paths, 0, args.length-5); | |
try { | |
OMEROWrapper reader = new OMEROWrapper(config); | |
ImportLibrary library = new ImportLibrary(store, reader); | |
ErrorHandler handler = new ErrorHandler(config); | |
IObserver status = new IObserver() { | |
public void update(IObservable importLibrary, ImportEvent event) { | |
if (event instanceof IMPORT_DONE) { | |
IMPORT_DONE ev = (IMPORT_DONE) event; | |
System.err.println("Imported pixels:"); | |
for (omero.model.Pixels p : ev.pixels) { | |
System.out.println(p.getId().getValue()); | |
} | |
} | |
} | |
}; | |
library.addObserver(status); | |
ImportCandidates candidates = new ImportCandidates(reader, paths, handler); | |
boolean success = library.importCandidates(config, candidates); | |
if (!success) { | |
System.err.println("Failed"); | |
} | |
} finally { | |
store.logout(); | |
} | |
} | |
} |
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